DoHeatmap: Feature expression heatmap

In satijalab/seurat: Tools for Single Cell Genomics

Feature expression heatmap

Description

Draws a heatmap of single cell feature expression.

Usage

DoHeatmap(
  object,
  features = NULL,
  cells = NULL,
  group.by = "ident",
  group.bar = TRUE,
  group.colors = NULL,
  disp.min = -2.5,
  disp.max = NULL,
  slot = "scale.data",
  assay = NULL,
  label = TRUE,
  size = 5.5,
  hjust = 0,
  vjust = 0,
  angle = 45,
  raster = TRUE,
  draw.lines = TRUE,
  lines.width = NULL,
  group.bar.height = 0.02,
  combine = TRUE
)

Arguments

object	Seurat object
features	A vector of features to plot, defaults to VariableFeatures(object = object)
cells	A vector of cells to plot
group.by	A vector of variables to group cells by; pass 'ident' to group by cell identity classes
group.bar	Add a color bar showing group status for cells
group.colors	Colors to use for the color bar
disp.min	Minimum display value (all values below are clipped)
disp.max	Maximum display value (all values above are clipped); defaults to 2.5 if slot is 'scale.data', 6 otherwise
slot	Data slot to use, choose from 'raw.data', 'data', or 'scale.data'
assay	Assay to pull from
label	Label the cell identies above the color bar
size	Size of text above color bar
hjust	Horizontal justification of text above color bar
vjust	Vertical justification of text above color bar
angle	Angle of text above color bar
raster	If true, plot with geom_raster, else use geom_tile. geom_raster may look blurry on some viewing applications such as Preview due to how the raster is interpolated. Set this to FALSE if you are encountering that issue (note that plots may take longer to produce/render).
draw.lines	Include white lines to separate the groups
lines.width	Integer number to adjust the width of the separating white lines. Corresponds to the number of "cells" between each group.
group.bar.height	Scale the height of the color bar
combine	Combine plots into a single patchworked ggplot object. If FALSE, return a list of ggplot objects

Value

A patchworked ggplot object if combine = TRUE; otherwise, a list of ggplot objects

Examples

data("pbmc_small")
DoHeatmap(object = pbmc_small)

satijalab/seurat documentation built on May 11, 2024, 4:04 a.m.